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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...epithelial-to-mesenchymal transition. Overall, ANS provides a robust and reliable gene signature scoring framework, significantly improving the accuracy of score-based annotation of cell types and states in single-cell studies.High-throughput single-cell RNA sequencing (scRNA-seq) is a powerful technology...
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Corrigendum: Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping
- Jordan A. Ramilowski,
- Chi Wai Yip,
- Saumya Agrawal,
- Jen-Chien Chang,
- Yari Ciani,
- Ivan V. Kulakovskiy,
- Mickaël Mendez,
- Jasmine Li Ching Ooi,
- John F. Ouyang,
- Nick Parkinson,
- Andreas Petri,
- Leonie Roos,
- Jessica Severin,
- Kayoko Yasuzawa,
- Imad Abugessaisa,
- Altuna Akalin,
- Ivan V. Antonov,
- Erik Arner,
- Alessandro Bonetti,
- Hidemasa Bono,
- Beatrice Borsari,
- Frank Brombacher,
- Christopher J.F. Cameron,
- Carlo Vittorio Cannistraci,
- Ryan Cardenas,
- Melissa Cardon,
- Howard Chang,
- Josée Dostie,
- Luca Ducoli,
- Alexander Favorov,
- Alexandre Fort,
- Diego Garrido,
- Noa Gil,
- Juliette Gimenez,
- Reto Guler,
- Lusy Handoko,
- Jayson Harshbarger,
- Akira Hasegawa,
- Yuki Hasegawa,
- Kosuke Hashimoto,
- Norihito Hayatsu,
- Peter Heutink,
- Tetsuro Hirose,
- Eddie L. Imada,
- Masayoshi Itoh,
- Bogumil Kaczkowski,
- Aditi Kanhere,
- Emily Kawabata,
- Hideya Kawaji,
- Tsugumi Kawashima,
- S. Thomas Kelly,
- Miki Kojima,
- Naoto Kondo,
- Haruhiko Koseki,
- Tsukasa Kouno,
- Anton Kratz,
- Mariola Kurowska-Stolarska,
- Andrew Tae Jun Kwon,
- Jeffrey Leek,
- Andreas Lennartsson,
- Marina Lizio,
- Fernando López-Redondo,
- Joachim Luginbühl,
- Shiori Maeda,
- Vsevolod J. Makeev,
- Luigi Marchionni,
- Yulia A. Medvedeva,
- Aki Minoda,
- Ferenc Müller,
- Manuel Muñoz-Aguirre,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Kazuhiro R. Nitta,
- Shuhei Noguchi,
- Yukihiko Noro,
- Ramil Nurtdinov,
- Yasushi Okazaki,
- Valerio Orlando,
- Denis Paquette,
- Callum J.C. Parr,
- Owen J.L. Rackham,
- Patrizia Rizzu,
- Diego Fernando Sánchez Martinez,
- Albin Sandelin,
- Pillay Sanjana,
- Colin A.M. Semple,
- Youtaro Shibayama,
- Divya M. Sivaraman,
- Takahiro Suzuki,
- Suzannah C. Szumowski,
- Michihira Tagami,
- Martin S. Taylor,
- Chikashi Terao,
- Malte Thodberg,
- Supat Thongjuea,
- Vidisha Tripathi,
- Igor Ulitsky,
- Roberto Verardo,
- Ilya E. Vorontsov,
- Chinatsu Yamamoto,
- Robert S. Young,
- J. Kenneth Baillie,
- Alistair R.R. Forrest,
- Roderic Guigó,
- Michael M. Hoffman,
- Chung Chau Hon,
- Takeya Kasukawa,
- Sakari Kauppinen,
- Juha Kere,
- Boris Lenhard,
- Claudio Schneider,
- Harukazu Suzuki,
- Ken Yagi,
- Michiel J.L. de Hoon,
- Jay W. Shin,
- and Piero Carninci
Genome Res. September 2020 30: 1377-1; doi:10.1101/gr.270330.120
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Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
...: why, where and how to stop. Nat Rev Mol Cell Biol 16: 190–202. doi:10.1038/nrm3943 ↵Ramilowski JA, Yip CW, Agrawal S, Chang J-C, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, et al. 2020. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 30...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...-nascent, now vast field of long noncoding RNA study (Mattick and Rinn 2015; Ramilowski et al. 2020). Not throwing data away but capturing and labeling it as well as possible has proved useful since the original annotation efforts. Even where transcript structures remain unchanged over the years (because...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...provides a blueprint for future annotation efforts of other organisms.ResultsGenerating accurate full-length cDNA data from 12 mouse tissuesWe constructed tissue-level, long-read transcriptome data using commercially available high-quality RNA (Takara Bio) from 12 mouse tissues (brain, eye, heart, kidney...
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Research: TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation
- Wenli Xu,
- Chang Liu,
- Bing Deng,
- Penghui Lin,
- Zhenghua Sun,
- Anrui Liu,
- Jiajia Xuan,
- Yuying Li,
- Keren Zhou,
- Xiaoqin Zhang,
- Qiaojuan Huang,
- Hui Zhou,
- Qingyu He,
- Bin Li,
- Lianghu Qu,
- and Jianhua Yang
Genome Res. June 2022 32: 1026-1041; Published in Advance May 24, 2022, doi:10.1101/gr.275831.121
....75%) annotated mRNAs, 1053 (16.99%) annotated lncRNAs, 422 (6.81%) annotated pseudogenes, and 152 (2.45%) other types of noncoding RNAs (Fig. 1C, top; Supplemental Table S1). The other comparison group was between WT-ADR+ and TP53−/−-ADR+ (|log2FC| ≥ 1; P < 0.05), which contained 3336 (71.47%) annotated mRNAs...
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Research: Preferential formation of Z-RNA over intercalated motifs in long noncoding RNA
- Uditi Bhatt,
- Anne Cucchiarini,
- Yu Luo,
- Cameron W. Evans,
- Jean-Louis Mergny,
- K. Swaminathan Iyer,
- and Nicole M. Smith
Genome Res. February 2024 34: 217-230; Published in Advance February 14, 2024, doi:10.1101/gr.278236.123
...of the structure–function relationship in lncRNAs.The discovery of long noncoding RNAs (lncRNAs) has revolutionized scientific understanding of the and has led to an explosion of research into the complex mechanisms that regulate gene expression. Currently, lncRNAs are broadly defined as any RNA >200 nt in length...
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Research: Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas
- Jonas Kjellin,
- Lotta Avesson,
- Johan Reimegård,
- Zhen Liao,
- Ludwig Eichinger,
- Angelika Noegel,
- Gernot Glöckner,
- Pauline Schaap,
- and Fredrik Söderbom
Genome Res. March 2021 31: 436-447; Published in Advance January 21, 2021, doi:10.1101/gr.272856.120
..., Dictyostelium discoideum. However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal...
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Research: Panoramic transcriptome analysis and functional screening of long noncoding RNAs in mouse spermatogenesis
- Kai Li,
- Jiayue Xu,
- Yanyun Luo,
- Dingfeng Zou,
- Ruiqin Han,
- Shunshun Zhong,
- Qing Zhao,
- Xinyu Mang,
- Mengzhen Li,
- Yanmin Si,
- Yan Lu,
- Pengyu Li,
- Cheng Jin,
- Zhipeng Wang,
- Fang Wang,
- Shiying Miao,
- Bo Wen,
- Linfang Wang,
- Yanni Ma,
- Jia Yu,
- and Wei Song
Genome Res. January 2021 31: 13-26; Published in Advance December 16, 2020, doi:10.1101/gr.264333.120
...; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China ↵3 These authors contributed equally to this work. Corresponding authors: songwei@ibms.pumc.edu.cn, j-yu@ibms.pumc.edu.cn, yanni_ma@126.comAbstractLong noncoding RNAs (lncRNAs) have...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...inhibitor JQ1 (Fig. 4). PRO-seq allows high-resolution mapping of active RNA polymerases across the at both coding and noncoding regions and provides information on both the abundance and directionality of transcripts. Analysis of the transcriptome in LBH589-treated ESCs revealed that the majority of genes...
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